1. Collaborative Construction of Large Biological Ontologies Jie Bao a , This work is in collaboration with Zhiliang Hu b , LaRon Hughes b , Doina Caragea c , Peter Wong a , James Reecy b , Vasant G Honavar a a Artificial Intelligence Research Laboratory, Department of Computer Science a Center for Computational Intelligence, Learning, and Discovery b Department of Animal Science, Iowa State University, Ames, IA 50011, USA c Department of Computing and Information Sciences, Kansas State University Manhattan, KS 66506 Email: {baojie, zhu, laron, pwwong,jreecy, honavar}@iastate.edu, dcaragea@ksu.edu

3. Large Biological Ontologies Gramineae Taxonomy Plant Ontology Gene Ontology MGED Ontology (microarray)

4. Example: Gene Ontology

5. Non-collaborative Ontology Building Download Ontology Local Editing Upload Ontology (single curator) (Protégé) (OBO-Edit)

6. Collaboration In Need Example: Gene Ontology Consortium

7. Collaboration In Need (2) Swine Cattle Chicken Horse Each group works on an ontology module for a particular species (according to the group’s best expertise) Example 2: an animal trait ontology that involves multiple research groups across the world

11. CVS-based Ontology Building Get GO CVS Account Get Source Forge Account Set Up CVS Access Submit Change Request Track the Request User submit change suggestion (in natural language) Get Source Forge Account Take a Change Request Curator Download Whole GO Flat File Local Editing Make Local Log File Save GO Flat File Manual Version Control Commit the Whole New Ontology to CVS

22. Partial Reuse General Cattle Pig Chicken Animal Trait Ontology (Centralized) Pork General Pig Cattle Chicken Pork Animal Trait Ontology (Package-based) Semantic importing Knowledge incorporated in Pork ontology Knowledge not presented in Prok ontology Legend:

26. The COB Editor Pig Package Cattle Package Chicken Package [Bao et al. BIDM06]